The X-Men are always dealing with something, and at the moment, Magneto is on trial for murdering the Scarlet Witch. He seems like the obvious suspect in the comics thanks to the bitter history between the Master of Magnetism and his former daughter, but there are clues that other major mutants may have been Wanda's killer.
Wanda's infamous actions during the House Of M storyline back in 2005 reverberate in the X-world today, generating massive enmity for her. But her death may not have been the result of hate or anger, but opportunity. Some characters may have killed Wanda to further their own ends, which could have disastrous consequences.
Agatha Harkness
Agatha Harkness is one of the most powerful magicians in the Marvel Universe and the former tutor of Wanda in magic. She's also been the victim of Wanda's anger, as Wanda killed Agatha in a fit of rage when she learned Agatha caused her to forget her children weren't real.
Agatha has since returned to the world of the living and while she might seem like a longshot - she wasn't on Krakoa, so far as anyone knows - she would have the motive, means and opportunity to have killed the Scarlet Witch.
Exodus
Early in the new era of X-Men comics, there is a scene where Exodus, an Omega-level mutant with psychic powers, recounts the events of House of M to a group of children. It's clear that he harbors no affection for the Scarlet Witch, who he calls "The Pretender."
Her arrival on Krakoa could have prompted him to lash out. His powers certainly fit the bill when it comes to the murder itself - she was dragged by an unseen force, bound, and choked without being able to defend herself. His telekinesis could have done that.
Mr. Sinister
Another member of the Quiet Council on Krakoa with an ulterior motive is Mr. Sinister. He may have no ill will toward her, but simply seek her genetic potential. Mr. Sinister is the architect of the cloning operation behind the Resurrection Protocols.
While Wanda's resurrection was voted down in The Trial Of Magneto #1, there is nothing to stop the greedy Mr. Sinister from either doing it himself or taking her own DNA for his own future use. Having the extraordinary power of the Scarlet Witch for his own designs would be reason enough to kill her.
Emma Frost
The White Queen is a power player through and through. She has risen to unimaginable influence on the White Council and likely seeks even more control. The best way for her to do that would be to pit its two patriarchs, Professor X and Magneto, against one another. Wanda's death has done that.
Emma Frost certainly could have killed the Scarlet Witch if she got the drop on her. She could have fooled Wanda with a mental manipulation or psychic illusion into thinking she was talking to Magneto and could have used her telekinetic blasts to accomplish the act itself.
Doctor Doom
Comic fans know Doctor Doom is always seeking more power. He's also threatened by it and as was clear during the Hellfire Gala, which he attended, he is wary of the growing power of Krakoa. Doom has sought to destabilize other nations before, most notably Wakanda in one of the best Black Panther comic book arcs, "Doomwar."
Just as Emma Frost could be trying to grab power, Doom could be seeking to throw Krakoa into chaos by killing the Scarlet Witch and implicating her father. Doom's impressive magic or one of his inventions could have made it look like Magneto was involved.
Moira MacTaggert
Moira MacTaggert has a lot to hide. The architect of the Krakoan era in Marvel Comics has barely been seen since her shocking revelation as a mutant in House Of X in 2019. Her motives in killing the Scarlet Witch could be as simple as protecting the fragile future she is trying so hard to build.
Moira is possibly on her last life, and any mistake now could cost her and mutants everything. She could perceive Wanda as being a threat, especially since Wanda is a Nexus Being and has the ability to alter reality, and Moira seems determined to be the one to control the reality of mutants.
Quicksilver
Quicksilver may seem an unlikely candidate given his love for his sister and his grief-stricken rage against Magneto in The Trial Of Magneto #1. Still, though he nearly beat Magneto to death, but he could have an ulterior motive.
Both Quicksilver and Scarlet Witch believed they were the children of Magneto and mutants for a long time. His murder of Wanda could be a way to resurrect her as a mutant and absolve her of the pain and suffering she's endured. He certainly has the speed and power to have killed her, even if it's unlikely.
Magneto
Magneto is the prime suspect in the comics and for good reason. He is the last person seen with Wanda, having invited her surreptitiously to the Hellfire Gala. Her hands were bound by metal, and the speed and scale of the attack suggest that someone with the ability to control metal could have killed her.
Like Quicksilver, he could have been motivated by a desire to resurrect Wanda as a mutant on Krakoa. He has also been vocal about his thoughts on her being a "pretender." But he also seems very adamant that it wasn't him.
Mystique
The most obvious suspect in Wanda's murder is Mystique. Mystique could have easily impersonated Magneto and likely did, since a very subtle clue suggests that the timeline of Wanda's murder is off.
Her death appears to have happened twenty minutes before she was seen with Magneto on Krakoa. Mystique's motivation is likely to throw Magneto and Professor X into chaos. The two have denied the resurrection of her wife Destiny, despite promises to do so, leaving Mystique embittered and seeking revenge.
The Scarlet Witch
An unexpected suspect in Wanda's death is Wanda herself. Like her brother or Magneto, Wanda could be seeking a resurrection to restore her as a mutant in her quest to atone for House Of M. While it's unlikely - though she has the reality-warping ability to have implicated Magneto in her own death - there is a chance.
Wanda has been shown not to be dead, but in some kind of limbo, possibly connected to Krakoa itself. She is surrounded by flowers and her magic and power could be interacting with the living island somehow.